[Fastacmd] How To Retrieve Sequence From Blast Db

Question

[Leszek]

Let's say I have multifasta with protein sequences having internal IDs (integer)

>1234
MGKL...*

I build blast db using:

formatdb -i infile.fa -pF -n someDB

But then, I'm unable to retrieve sequence from db using simple protein id:

fastacmd -d someDB -s 1234

How to define fasta header so I can retrieve sequences easily?
I have noticed formatdb assign internal identifiers (increment int) to my sequences, and orginal ID appears later:

>gnl|BL_ORD_ID|12 1234

Why is that?

I then defined headers as:

>gnl|dbname|1234

but with no effect. Do I have to define headers as >gi|1234 in order to be able to get sequence? Or is there any other way of retrieving sequences from blast db?

Answer 1

[Naga]

With formatdb command use "-o" option to create indexes from the protein ID (IDs should be unique to create indexes)

[?] -o Parse options T - True: Parse SeqId and create indexes. F - False: Do not parse SeqId. Do not create indexes [T/F] Optional default = F [?][?] formatdb -i infile.fa -pF -n someDB -o T [?]

and then you can use "-s" option in fastacmd to retrieve single sequence.

[Leszek]

och, stupid me! I didn't noticed that parameter. thanks a lot Nagarajan